Results 11 to 20 of about 297,066 (279)

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields. [PDF]

Acta Crystallogr D Struct Biol
In macromolecular structure refinement, the low observation-to-parameter ratio and the lack of high-resolution data are countered by using a priori information in the form of restraints. Having accurate geometries of the chemical entities in the sample is paramount for generating accurate ...
Moriarty NW, Case DA, Liebschner D, Adams PD.   +3 more
europepmc   +7 more sources

Keep it together: restraints in crystallographic refinement of macromolecule–ligand complexes [PDF]

Acta Crystallographica Section D Structural Biology, 2017
A short introduction is provided to the concept of restraints in macromolecular crystallographic refinement. A typical ligand restraint-generation process is then described, covering types of input, the methodology and the mechanics behind the software in general terms, how this has evolved over recent years and what to look for in the output. Finally,
Steiner R., Tucker J. A.
openaire   +6 more sources

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix [PDF]

Acta Crystallographica Section D Structural Biology, 2019
The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models.
Nigel W. Moriarty, Pawel A. Janowski, Jason M. Swails, Hai Nguyen, Jane S. Richardson, David A. Case, Paul D. Adams   +6 more
openaire   +9 more sources

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution [PDF]

Acta Crystallographica Section D Biological Crystallography, 2012
Traditional methods for macromolecular refinement often have limited success at low resolution (3.0–3.5 Å or worse), producing models that score poorly on crystallographic and geometric validation criteria. To improve low-resolution refinement, knowledge from macromolecular chemistry and homology was used to add three new coordinate-restraint functions
Jeffrey J. Headd, Nathaniel Echols, Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Vincent B. Chen, Nigel W. Moriarty, David C. Richardson, Jane S. Richardson, Paul D. Adams   +8 more
openaire   +6 more sources

Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement [PDF]

Acta Crystallographica Section D Biological Crystallography, 2014
One of the great challenges in refining macromolecular crystal structures is a low data-to-parameter ratio. Historically, knowledge from chemistry has been used to help to improve this ratio. When a macromolecule crystallizes with more than one copy in the asymmetric unit, the noncrystallographic symmetry relationships can be exploited to provide ...
Headd, Jeffrey J, Echols, Nathaniel, Afonine, Pavel V, Moriarty, Nigel W, Gildea, Richard J, Adams, Paul D   +5 more
openaire   +6 more sources

Impact of Refinements to Handling and Restraint Methods in Mice

Animals, 2022
There is increasing evidence that, compared to non-aversive handling methods (i.e., tunnel and cupping), tail handling has a negative impact on mouse welfare. Despite this evidence, there are still research organisations that continue to use tail handling.
Jennifer R. Davies, Dandri A. Purawijaya, Julia M. Bartlett, Emma S. J. Robinson   +3 more
openaire   +3 more sources

Refining restraint techniques for research pigs through habituation

Frontiers in Veterinary Science, 2022
Pigs are common research models and are strong animals that can be difficult to restrain. Improper restraint can put pigs and research personnel at risk for injury and induce stress, which can affect research outcomes. This study aimed to refine restraint techniques for research pigs using habituation and operant conditioning.
Carly I. O'Malley, Raina Hubley, Halimatou Tambadou, Patricia V. Turner, Patricia V. Turner   +4 more
openaire   +3 more sources

On the complexity of Engh and Huber refinement restraints: the angle τ as example [PDF]

Acta Crystallographica Section D Biological Crystallography, 2010
The Engh and Huber parameters for bond lengths and bond angles have been used uncontested in macromolecular structure refinement from 1991 until very recently, despite critical discussion of their ubiquitous validity by many authors. An extensive analysis of the backbone angle τ (N-C(α)-C) illustrates that the Engh and Huber parameters can indeed be ...
Touw, W.G., Vriend, G., Vriend, G.
openaire   +3 more sources

Pseudo-CSA Restraints for NMR Refinement of Nucleic Acid Structure [PDF]

Journal of the American Chemical Society, 2006
Upon alignment of oligonucleotides in a magnetic field, the downfield TROSY component of the 13C-{1H} doublet changes its resonance frequency as a result of residual 13C-1H dipolar coupling (RDC) and residual 13C chemical shift anisotropy (RCSA), and the sum of these two second rank tensors is referred to as the pseudo-CSA.
Alexander, Grishaev, Jinfa, Ying, Ad, Bax   +2 more
openaire   +2 more sources

NMR Refinement and Peptide Folding Using the GROMACS Software [PDF]

, 2021
Nuclear magnetic resonance spectroscopy is used routinely for studying the three-dimensional structures and dynamics of proteins. Structure determination is usually done by adding restraints based upon NMR data to a classical energy function and ...
David, van der Spoel, Sinelnikova, Anna, Anna, Sinelnikova, Van der Spoel, David, Sinelnikova, Anna,, Van der Spoel, David,   +5 more
core   +1 more source